Contacts of the helix formed by residues 291 - 302 (chain C) in PDB entry 4BPU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP 291 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LEU* 4.2 19.7 - - + -
205C SER 3.3 27.5 + - - -
206C GLU* 3.6 21.4 + - - +
208C ILE* 4.1 13.8 - - + +
290C PRO* 1.3 88.5 - - + +
292C LEU* 1.3 63.4 + - - +
293C GLU* 3.2 3.4 - - - -
294C TRP* 3.1 49.8 + + + -
295C GLU* 3.1 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C LYS* 4.7 2.7 - - - +
246C LEU 3.7 21.8 - - - +
247C VAL* 3.6 26.0 - - + -
248C PRO* 3.7 25.4 - - + -
251C ILE* 4.2 11.4 - - + -
272C LEU* 5.3 1.6 - - + -
276C ALA* 4.6 19.8 - - + +
279C TYR* 4.8 12.1 - - + -
290C PRO* 3.0 25.2 + - + +
291C TRP* 1.3 73.8 - - - +
293C GLU* 1.3 63.0 + - - +
295C GLU* 3.1 19.0 + - - +
296C ILE* 2.9 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 293 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C LYS* 4.6 8.5 - - - -
269C TRP* 3.5 30.2 + - + -
272C LEU* 4.5 10.5 - - + +
273C LYS* 3.5 39.2 - - + +
276C ALA* 4.9 8.7 - - + +
277C SER* 5.2 3.5 + - - -
291C TRP 3.1 1.2 + - - -
292C LEU* 1.3 79.9 - - - +
294C TRP* 1.3 81.0 + - + +
296C ILE 3.5 0.3 + - - -
297C MET* 3.2 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 294 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LEU* 4.0 5.4 - - + -
208C ILE* 4.3 20.0 - - + -
213C ARG* 6.1 5.2 - - + -
216C ILE* 3.7 50.5 - - + +
217C ASN* 6.1 0.7 - - - -
220C LYS* 3.9 25.3 - - - +
291C TRP* 3.1 50.7 + + + +
293C GLU* 1.3 88.5 + - + +
295C GLU* 1.3 59.6 + - - +
297C MET* 3.3 17.8 + - - +
298C LEU* 2.9 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C LYS* 2.4 45.0 + - - +
202C VAL* 3.6 24.4 - - + +
203C HIS* 3.7 2.6 - - - +
204C LEU* 2.9 47.1 + - + +
246C LEU* 5.5 0.2 - - - -
290C PRO* 4.2 12.3 - - - +
291C TRP 3.1 19.8 + - - +
292C LEU* 3.5 18.9 - - - +
294C TRP* 1.3 76.5 - - - +
296C ILE* 1.3 56.7 + - - +
298C LEU* 4.5 0.2 - - - -
299C GLN* 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C LYS* 5.9 0.2 - - - +
223C PHE* 5.1 4.3 - - + -
233C ILE* 5.1 0.4 - - + -
243C ILE* 3.8 19.1 - - + -
246C LEU* 4.0 24.9 - - + +
247C VAL* 4.3 13.9 - - + -
269C TRP* 4.0 17.0 - - + -
272C LEU* 3.8 37.9 - - + -
292C LEU* 2.9 22.8 + - - +
293C GLU 3.9 3.6 - - - +
295C GLU* 1.3 76.3 - - + +
297C MET* 1.3 59.9 + - - +
299C GLN* 3.2 4.8 + - - +
300C TYR* 2.8 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ILE* 4.6 7.9 - - + +
219C ILE* 4.1 13.7 - - + -
220C LYS* 3.6 44.6 - - + +
223C PHE* 3.8 36.8 - - + -
269C TRP* 3.9 12.1 - - + -
293C GLU* 3.2 30.9 + - - +
294C TRP* 3.3 24.2 + - - +
296C ILE* 1.3 75.3 - - - +
298C LEU* 1.3 54.5 + - + +
300C TYR 3.1 1.4 + - - -
301C CYS* 2.7 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C LEU* 4.0 10.3 - - + -
192C VAL* 4.2 1.4 - - - +
202C VAL* 4.1 19.7 - - + -
204C LEU* 3.9 25.4 - - + -
212C ILE* 3.9 17.3 - - + -
215C SER* 5.0 0.4 - - - -
216C ILE* 4.0 22.4 - - + +
219C ILE* 3.8 13.7 - - + -
294C TRP 2.9 22.6 + - - +
295C GLU 3.9 3.6 - - - +
297C MET* 1.3 76.4 - - + +
299C GLN* 1.3 61.1 + - - +
302C PHE* 2.8 63.1 + - + +
304C ARG* 4.1 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ASP* 5.2 2.2 + - - -
118C VAL* 3.7 5.9 - - + +
192C VAL* 4.8 1.6 - - - -
199C LYS 2.7 28.1 + - - -
200C LYS* 3.7 4.5 + - - +
201C LYS* 3.0 40.8 + - + +
202C VAL* 3.6 15.9 + - + +
246C LEU* 3.5 27.9 - - + +
295C GLU 2.8 20.1 + - - +
296C ILE* 3.6 6.7 - - - +
298C LEU* 1.3 76.7 - - - +
300C TYR* 1.3 63.3 + - + +
304C ARG* 3.1 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C TYR* 4.9 0.5 - - - -
117C ASP 5.0 3.2 + - - -
118C VAL* 3.7 53.0 - - + +
120C ARG* 6.3 1.6 - - + -
134C LEU* 3.4 17.0 - - - +
223C PHE* 4.6 7.4 - - + -
226C TYR* 4.1 8.6 + + + -
227C ALA* 5.7 0.2 - - + -
233C ILE* 3.8 32.3 + - + +
239C SER 4.6 1.9 + - - -
242C LYS* 3.8 23.1 - - - +
243C ILE* 3.8 28.9 - - + +
246C LEU* 4.1 15.7 - - + -
296C ILE* 2.8 31.0 + - + +
297C MET 3.9 2.0 - - - +
299C GLN* 1.3 87.9 - - + +
301C CYS* 1.3 66.9 + - - +
304C ARG* 4.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C TYR* 4.7 2.0 - - - -
134C LEU* 3.9 13.9 - - - +
137C MET* 3.7 29.1 - - + +
219C ILE* 3.6 21.7 - - + +
223C PHE* 3.6 33.4 - - - -
226C TYR* 3.8 24.2 - - - -
297C MET 2.7 17.6 + - - +
300C TYR* 1.3 80.8 - - - +
302C PHE* 1.3 65.4 + - - +
303C PRO* 3.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 302 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C TYR* 3.7 5.0 - - - -
141C ILE* 3.8 14.6 - - + -
142C ILE* 6.2 0.2 - - + -
189C LEU 3.2 27.4 - - - -
191C LEU* 3.5 42.2 - - + -
192C VAL* 4.1 8.5 - - + +
211C PHE* 3.8 10.8 - + - -
215C SER* 3.8 22.0 - - - -
219C ILE* 4.0 3.1 - - - +
298C LEU* 2.8 47.8 + - + +
301C CYS* 1.3 79.1 - - - +
303C PRO* 1.4 106.6 - - + +
304C ARG* 3.1 21.8 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il